BETY cleanup

[infotroph]

Dealing with bits from the BETY API version update that weren't finished in #82.

• Read bety instance URL, API version, and key from options (probably closes Refactor generic betydb functions to use new BETYdb API #77)
  • @dlebauer Does this usage work? We discussed it a bit in Refactor Betydb functions to support new API #82, but didn't make a firm decision. I went with options("betydb_url") etc over list(url, version, key, ...) because it appears to be more in line with how auth is handled in other ropensci packages.
  • @sckott I'd appreciate a skeptical review of my test case. I wanted to ensure that all option changes get rolled back at the end of the test_that, which turns out to be more complicated than I expected. See any lurking bugs?
• Document that betydb_query accepts include_unchecked, limit, and offset (Add option to retrieve 'unchecked' data from BETYdb #52 )
• Deprecate table-specific query functions (Merge BETYdb table queries into a single generic function #26)?
  • As discussed in Use cases for non-ID search fields in singular betydb_* functions #84, betydb_record now provides a generic replacement, so betydb_<table>(id) is now ~equivalent to betydb_record(id, table=<table>).
  • A possible argument for retention: Would these functions be the appropriate place to handle output standardization (Standardize data.frame's across data sources #38)? Records queried through the beta API contain nested lists whose layout differs from one table to another, so maybe they become formatters: Have betydb_<table> call betydb_record to get the full possibly-nested list, then apply whatever table-specific formatting is needed to return a standardized dataframe.

[codecov-io]

Codecov Report

❗ No coverage uploaded for pull request base (master@5af13de). Click here to learn what that means.
The diff coverage is 100%.

@@            Coverage Diff            @@
##             master      #88   +/-   ##
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  Coverage          ?   12.98%           
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  Files             ?       14           
  Lines             ?      716           
  Branches          ?        0           
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  Hits              ?       93           
  Misses            ?      623           
  Partials          ?        0

Impacted Files	Coverage Δ
R/betydb.R	96.66% <100%> (ø)

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[sckott]

@infotroph sure, i'll have a look

[dlebauer]

Using options makes sense to me - I'll defer to the ropensci conventions & best practices

…

On Fri, Feb 24, 2017 at 4:01 PM Scott Chamberlain ***@***.***> wrote: @infotroph <https://github.com/infotroph> sure, i'll have a look — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#88 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAcX5w1pyR_tqgePBLIMRvt7m47v-yKrks5rf1MqgaJpZM4MLdQH> .

[sckott]

@infotroph

in the future it'd be easier to deal with smaller PR's - this isn't huge, but does encompass things that at least to me could be done separately.

Looks okay to me for now. we'll see later if it leads to any problems, travis is passing, so that's a good sign

[infotroph]

@sckott sorry for the huge pull -- I'm making a note to keep them smaller in the future. This can be merged now and I'll submit deprecation changes separately iff we go forward with them.

[sckott]

thanks @infotroph